1. 23 Apr, 2015 1 commit
  2. 08 Jan, 2015 1 commit
  3. 16 Oct, 2014 1 commit
  4. 08 Oct, 2014 1 commit
  5. 02 Sep, 2014 1 commit
    • Tiago Peixoto's avatar
      Implement new binary graph format "gt" · d0d247ea
      Tiago Peixoto authored
      The new format fully supports all property map types present in
      graph-tool and should be much faster and produce smaller files than the
      other text-based formats.
      d0d247ea
  6. 06 Aug, 2014 1 commit
  7. 02 Jan, 2014 1 commit
  8. 10 Nov, 2013 1 commit
  9. 11 Feb, 2013 1 commit
  10. 06 Jan, 2013 1 commit
  11. 02 Dec, 2012 1 commit
  12. 27 Oct, 2012 1 commit
  13. 09 Jul, 2012 1 commit
  14. 02 May, 2012 1 commit
  15. 31 Mar, 2012 1 commit
  16. 21 Mar, 2012 2 commits
  17. 01 Jun, 2011 1 commit
  18. 10 Feb, 2011 1 commit
  19. 02 Feb, 2011 1 commit
  20. 04 Dec, 2010 1 commit
    • Tiago Peixoto's avatar
      Improve behaviour of property map type conversion · 897f454f
      Tiago Peixoto authored
      Now an explicit conversion to a compatible python type is attempted if
      the value being set in a property map cannot be converted directly to a
      C++ type.
      
      This also fixes a bug with vector-valued property maps.
      897f454f
  21. 13 Nov, 2010 1 commit
  22. 07 Mar, 2010 1 commit
  23. 05 Nov, 2009 1 commit
  24. 18 Sep, 2009 1 commit
    • Tiago Peixoto's avatar
      Edge and vertex descriptors now carry a weakref to their Graphs · c6c01d62
      Tiago Peixoto authored
      This fixes an obvious problem, where the graph gets deleted, and the
      descriptors are still lying around. Usage of orphaned descriptors will
      now just raise a ValueError.
      
      The __repr__ function of Edge, Vertex, and PropertyMap now give
      something more informative about each object.
      c6c01d62
  25. 21 Aug, 2009 1 commit
    • Tiago Peixoto's avatar
      Dump lambda::bind in favor of boost::bind · 7fb5d71d
      Tiago Peixoto authored
      This is a large commit which replaces lambda::bind with boost::bind in
      most parts of the code. This improves compilation time, and slightly
      decreases compilation memory usage in some cases.
      7fb5d71d
  26. 16 Aug, 2009 1 commit
  27. 13 Aug, 2009 1 commit
    • Tiago Peixoto's avatar
      Reorganize exceptions thrown · f257d426
      Tiago Peixoto authored
      No longer only thrown GraphError upon any error, but instead throw
      specific exceptions which are more meaninful and are mapped to standard
      python exceptions, such as IOError, ValueError and RuntimeError.
      f257d426
  28. 15 May, 2009 1 commit
  29. 10 Mar, 2009 1 commit
    • Tiago Peixoto's avatar
      Implement optional wrapping of graphs to deal with edge index housekeeping · 684efca7
      Tiago Peixoto authored
      Thins changes the graph filtering code slightly to wrap graph types with
      GraphWrap, which automatically updates the edge index list when edges
      are removed and added to the graph.
      
      This also changes how graphs are passed to algorithms, which is now by
      reference instead of pointer. (hence this touches lots of code, but
      changes are trivial)
      684efca7
  30. 06 Feb, 2009 3 commits
    • Tiago Peixoto's avatar
      Fix get_array() for property maps · 548d61bb
      Tiago Peixoto authored
      This includes the missing function declarations for edge and graph
      properties.
      
      Property maps of value type "string" do not return an array, since the
      numpy string and std::string are different things.
      548d61bb
    • Tiago Peixoto's avatar
      Disable internal bounds checking in property maps · 0ababf9c
      Tiago Peixoto authored
      This includes a new vector property map type (fast_vector_property_map)
      which has optional disabling of bounds checking, through its associate
      map type (unchecked_fast_vector_property_map). This should improve
      performance on algorithms which depend on tight loops which access
      property maps.
      
      Bounds checking is only disabled locally just before the algorithms run,
      and proper care is taken for bounds checking _beforehand_. The property
      maps exposed to python still have internal bounds checking.
      0ababf9c
    • Tiago Peixoto's avatar
      Add support for array access to property maps · e84aaf3c
      Tiago Peixoto authored
      A property map object has now a get_array() member which returns an internally
      owned array pointing to the property values.
      e84aaf3c
  31. 02 Dec, 2008 1 commit
  32. 17 Jun, 2008 1 commit
    • Tiago Peixoto's avatar
      Externalize property maps by default · e984bf8e
      Tiago Peixoto authored
      This commit removes the internal property maps from the GraphInterface
      class, and makes all property maps external by default. The internal
      property maps were moved to the python layer.
      e984bf8e
  33. 06 May, 2008 1 commit
  34. 10 Apr, 2008 1 commit
    • Tiago Peixoto's avatar
      Correlations algorithms refactoring · 360a3395
      Tiago Peixoto authored
      The whole histogram code has been redone, and the code has been
      simplified. The three-point vertex-edge-vertex correlation has been
      scrapped, since it's not frequently used, and would make compilation
      even more expensive.
      
      This also adds some missing files to the generation routine.
      360a3395
  35. 27 Mar, 2008 1 commit
    • Tiago Peixoto's avatar
      Port graph I/O to new filtering engine, enable graph pickling, and fix several issues · 99bf21c8
      Tiago Peixoto authored
      Now graphml files properly contain all the supported value types, which
      are all perfectly preserved when read (floating point data is now saved
      in hexadecimal format). Several other improvements were made, such as
      the ability to read and write to python file-like objects.
      
      It is also now possible to have arbitrary python object properties, and
      store them persistently (which is done internally with the pickling
      interface).
      
      vector<bool> was totally abolished, since its implementation is quite
      broken. See: http://www.gotw.ca/publications/N1211.pdf and
      http://www.gotw.ca/publications/N1185.pdf Now a uint8_t (aka. char) is
      used in graph properties instead of a bool.
      
      Graph types can now be fully pickled (this may not be feasible
      memory-wise if the graph is too large, since the whole XML
      representation is dumped to a string before it is saved on disc).
      99bf21c8
  36. 17 Feb, 2008 1 commit
    • Tiago Peixoto's avatar
      Split libgraph_tool into sub-modules and add test cases · 3cfff0cb
      Tiago Peixoto authored
      This commit splits libraph_tool into different libraries:
       
         - libgraph_tool_core
         - libgraph_tool_clustering (*)
         - libgraph_tool_community (*)
         - libgraph_tool_correlations (*)
         - libgraph_tool_distance (*)
         - libgraph_tool_generation (*)
         - libgraph_tool_layout (*)
         - libgraph_tool_misc (*)
         - libgraph_tool_stats (*)
      
      It also adds the python sub-module 'test', which provides extensive unit
      testing of the core functionality. The core library is fully functional
      and all test pass successfully.
      
      (*) -> module needs to be ported to new refactoring, and does not yet build
      3cfff0cb
  37. 10 Feb, 2008 1 commit
    • Tiago Peixoto's avatar
      Refactor metaprogramming engine · 0b66e272
      Tiago Peixoto authored
      This is a huge commit which completely refactors the metaprogramming
      engine which generates and selects (at run time) the graph view type and
      the desired algorithm implementation (template instantiation) that runs
      on it.
      
      Things are laid out now as following. There exists a main underlying
      graph type (GraphInterface::multigraph_t) and several other template
      classes that mask it some way or another, in a hierarchic fashion:
      
           multigraph_t -> filtered_graph (edges only, vertices only, both)
               |                               |           |           |
               |                               |           |           |
               |-------(reversed_graph)--------|-----------|-----------|
               |                               |           |           |
               \------(UndirectedAdaptor)------------------------------/
      
      The filtered_graph filters out edges and/or vertices from the graph
      based on some scalar boolean property. The reversed_graph reversed the
      direction of the edges and, finally, the UndirectedAdaptor treats the
      original directed graphs as undirected, transversing the in- and
      out-edges of each vertex indifferently. Thus, the total number of graph
      view types is 12. (The option --disable-graph-filtering can be passed to
      the configure script, which will disable graph filtering altogether and
      bring the total number down to 3, to reduce compile time and memory
      usage)
      
      In general, some specific algorithm, implemented as a template function
      object, needs to be instantiated for each of those types. Furthermore,
      the algorithm may also depend on other types, such as specific
      property_maps. Thus, the following scheme is used:
      
          struct my_algorithm // algorithm to be implemented
          {
              template <class Graph, class PropertyMap>
              void operator()(Graph *g, PropertyMap p, double& result) const
              {
                  // ...
              }
          };
      
          // in order for the above code to be instantiated at compile time
          // and selected at run time, the run_action template function object
          // is used from a member function of the GraphInterface class:
      
          double GraphInterface::MyAlgorithm(string prop_name)
          {
              double result;
              boost::any vprop = prop(property, _vertex_index, _properties);
              run_action<>()(*this, bind<void>(my_algorithm(), _1, _2,
                                               var(result)),
                             vertex_scalar_properties())(vprop);
              return result;
          }
      
      The whole code was changed to reflect this scheme, but now things are
      more centralized and less ad-hoc code needed to be
      written. Unfortunately, due to GCC's high memory usage during template
      instantiations, some of the code (namely all the degree correlation
      things) had to be split in multiple compilation units... Maybe this will
      change in the future if GCC gets optimized.
      
      This commit also touches other parts of code. More specifically, the way
      filtering gets done is very different. Now we only filter on boolean
      properties, and with the above scheme, the desired implementation runs
      with the correct chosen type, and no implicit type conversions should
      ever happen, which would have a bad impact on performance.
      0b66e272